Twin studies and λs (=5.0) of Alzheimer’s disease indicate that genetic risk factors are thought to contribute the development and progression. SNP-based genome-wide association studies have been intensively done. As the most of risk SNPs identified are only small effect on the disease, the family-based genome analysis has been re-evaluated. The next generation sequencing proved to be a new powerful tool to determine rare variants in patents with family history. In addition to genome sequencing, we performed gene expression analysis of human brains diagnosed as to senile plaques and neurofibrillary tangles by the exon-array and next generation sequencing. It should be innovated the possible mechanism that gene expression is regulated by a gene-gene cluster between distal regions on the same chromosome or on a different chromosome, and alternatively by non-coding RNA including microRNA.